Alignments for a candidate for dapF in Pseudomonas simiae WCS417

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate GFF5388 PS417_27585 diaminopimelate epimerase

Query= SwissProt::P44859
         (274 letters)



>FitnessBrowser__WCS417:GFF5388
          Length = 276

 Score =  322 bits (824), Expect = 7e-93
 Identities = 157/274 (57%), Positives = 200/274 (72%)

Query: 1   MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHY 60
           ++F+KMHGLGNDF+V+D V+Q+    P+  ++  +RH GIGFDQLLIVEAP +PE+DF Y
Sbjct: 3   LRFTKMHGLGNDFMVLDLVSQHAHILPKHAKQWGDRHTGIGFDQLLIVEAPSNPEVDFRY 62

Query: 61  RIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGE 120
           RIFNADGSEV QCGNGARCFARFV  K LT K+ I V T+ G + L ++ D QI VNMG 
Sbjct: 63  RIFNADGSEVEQCGNGARCFARFVLDKRLTAKRQIRVETKSGVIELDIRSDGQISVNMGA 122

Query: 121 PIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLE 180
           P   PA IPF A +   +Y L  D +TV   AVSMGNPH V++V+DI  A V +LGP +E
Sbjct: 123 PRLVPADIPFQAPEQAASYALDVDGKTVEIAAVSMGNPHAVLRVNDINNAPVHELGPKIE 182

Query: 181 SHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQV 240
            H RFP RVN GF+Q+I++   +LRV+ERGAGETQACG+GACAA    I QG +++ + +
Sbjct: 183 HHPRFPARVNVGFLQVIDRTRAQLRVWERGAGETQACGTGACAAAVAAISQGWMDSPLLI 242

Query: 241 DLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL 274
           DLPGG L IEW G GHP+ MTG A+ +Y+G + L
Sbjct: 243 DLPGGRLSIEWAGPGHPVMMTGPASRVYEGQVRL 276


Lambda     K      H
   0.321    0.139    0.423 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 259
Number of extensions: 6
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 274
Length of database: 276
Length adjustment: 25
Effective length of query: 249
Effective length of database: 251
Effective search space:    62499
Effective search space used:    62499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate GFF5388 PS417_27585 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.3315.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.3315.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.